Statistical coil model of the unfolded state: Resolving the reconciliation problem

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 37, 2005, Pages 13099-13104

  Jha, Abhishek K ^a,b   Colubri, Andrés ^a,b   Freed, Karl F ^a,c   Sosnick, Tobin R ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

Denatured state; Nearest neighbor; Protein folding; Radius of gyration; Residual dipolar coupling

Indexed keywords

PROLINE;

ARTICLE; BETA CHAIN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN DENATURATION; PROTEIN FOLDING; SIGNAL TRANSDUCTION; STATISTICAL MODEL; THERMODYNAMICS;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; MODELS, STATISTICAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

EID: 24944542708     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0506078102     Document Type: Article

References (49)

1. Shortle, D. & Ackerman, M. S. (2001) Science 293, 487-489.
2. Prestegard, J. H., Al-Hashimi, H. M. & Tolman, J. R. (2000) Q. Rev. Biophys. 33, 371-424.
3. Bax, A. (2003) Protein Sci. 12, 1-16.
4. Tjandra, N. (1999) Struct. Folding Des. 7, R205-R211.
5. Meiler, J., Blomberg, N., Nilges, M. & Griesinger, C. (2000) J. Biomol. NMR 16, 245-252.
6. Skrynnikov, N. R. & Kay, L. E. (2000) J. Biomol. NMR 18, 239-252.
7. Delaglio, F., Kontaxis, G. & Bax, A. (2000) J. Am. Chem. Soc. 122, 2142-2143.
8. Kohn, J. E., Millett, I. S., Jacob, J., Zagrovic, B., Dillon, T. M., Cingel, N., Dothager, R. S., Seifert, S., Thiyagarajan, P., Sosnick, T. R., et al. (2004) Proc. Natl. Acad. Sci. USA 101, 12491-12496.
9. Ohnishi, S. & Shortle, D. (2003) Protein Sci. 12, 1530-1537.
10. Ohnishi, S., Lee, A. L., Edgell, M. H. & Shortle, D. (2004) Biochemistry 43, 4064-4070.
11. Fieber, W., Kristjansdottir, S. & Poulsen, F. M. (2004) J. Mol. Biol. 339, 1191-1199.
12. Tanford, C., Kawahara, K. & Lapanje, S. (1966) J. Biol. Chem. 241, 1921-1923.
13. Tanford, C. (1968) Adv. Protein Chem. 23, 121-282.
14. Millet, I. S., Doniach, S. & Plaxco, K. W. (2002) Adv. Protein Chem. 62, 241-262.
15. Freed, K. F. (1987) Renormalization Group Theory of Macromolecules (Wiley Interscience, New York).
16. Tran, H. T., Wang, X. & Pappu, R. V. (2005) Biochemistry, 10.1021/bi0501961.
17. Fitzkee, N. C. & Rose, G. D. (2004) Proc. Natl. Acad. Sci. USA 101, 12497-12502.
18. Jacob, J., Krantz, B., Dothager, R. S., Thiyagarajan, P. & Sosnick, T. R. (2004) J. Mol. Biol. 338, 369-382.
19. Swindells, M. B., MacArthur, M. W. & Thornton, J. M. (1995) Nat. Struct. Biol. 2, 596-603.
20. Smith, L. J., Bolin, K. A., Schwalbe, H., MacArthur, M. W., Thornton, J. M. & Dobson, C. M. (1996) J. Mol. Biol. 255, 494-506.
21. Munoz, V. & Serrano, L. (1994) Proteins 20, 301-311.
22. Smith, L. J., Fiebig, K. M., Schwalbe, H. & Dobson, C. M. (1996) Fold Des. 1, R95-R106.
23. Penkett, C. J., Redfield, C., Dodd, I., Hubbard, J., McBay, D. L., Mossakowska, D. E., Smith, R. A., Dobson, C. M. & Smith, L. J. (1997) J. Mol. Biol. 274, 152-159.
24. Shi, Z., Olson, C. A., Rose, G. D., Baldwin, R. L. & Kallenbach, N. R. (2002) Proc. Natl. Acad. Sci. USA 99, 9190-9195.
25. Jha, A. K., Colubri, A., Zaman, M. H., Koide, S., Sosbick, T. R. & Freed, K. F. (2005) Biochemistry 44, 9691-9702.
26. Ohnishi, S. & Shortle, D. (2003) Proteins 50, 546-551.
27. Ackerman, M. S. & Shortle, D. (2002) Biochemistry 41, 3089-3095.
28. Ackerman, M. S. & Shortle, D. (2002) Biochemistry 41, 13791-13797.
29. Mohana-Borges, R., Goto, N. K., Kroon, G. J., Dyson, H. J. & Wright, P. E. (2004) J. Mol. Biol. 340, 1131-1142.
30. Ding, K., Louis, J. M. & Gronenborn, A. M. (2004) J. Mol. Biol. 335, 1299-1307.
31. Tycko, R., Blanco, F. J. & Ishii, Y. (2000) J. Am. Chem. Soc. 122, 9340-9341.
32. Plaxco, K. W. & Gross, M. (2001) Nat. Struct. Biol. 8, 659-660.
33. Louhivuori, M., Paakkonen, K., Fredriksson, K., Permi, P., Lounila, J. & Annila, A. (2003) J. Am. Chem. Soc. 125, 15647-15650.
34. Sallum, C. O., Martel, D. M., Fournier, R. S., Matousek, W. M. & Alexandrescu, A. T. (2005) Biochemistry 44, 6392-6403.
35. Zaman, M. H., Shen, M. Y., Berry, R. S., Freed, K. F. & Sosnick, T. R. (2003) J. Mol. Biol. 331, 693-711.
36. Pappu, R. V., Srinivasan, R. & Rose, G. D. (2000) Proc. Natl. Acad. Sci. USA 97, 12565-12570.
37. Keskin, O., Yuret, D., Gursoy, A., Turkay, M. & Erman, B. (2004) Proteins 55, 992-998.
38. Gibrat, J. F., Garnier, J. & Robson, B. (1987) J. Mol. Biol. 198, 425-443.
39. Kang, H. S., Kurochkina, N. A. & Lee, B. (1993) J. Mol. Biol. 229, 448-460.
40. Avbelj, F. & Baldwin, R. L. (2004) Proc. Natl. Acad. Sci. USA 101, 10967-10972.
41. Wang, G. & Dunbrack, R. L., Jr. (2003) Bioinformatics 19, 1589-1591.
42. Canutescu, A. A., Shelenkov, A. A. & Dunbrack, R. L., Jr. (2003) Protein Sci. 12, 2001-2014.
43. Word, J. M., Lovell, S. C., Richardson, J. S. & Richardson, D. C. (1999) J. Mol. Biol. 285, 1735-1747.
44. Haber, C., Ruiz, S. A. & Wirtz, D. (2000) Proc. Natl. Acad. Sci. USA 97, 10792-10795.
45. Eker, F., Griebenow, K. & Schweitzer-Stenner, R. (2003) J. Am. Chem. Soc. 125, 8178-8185.
46. Chellgren, B. W. & Creamer, T. P. (2004) Biochemistry 43, 5864-5869.
47. Dukor, R. K. & Keiderling, T. A. (1991) Biopolymers 31, 1747-1761.
48. Gillespie, J. R. & Shortle, D. (1997) J. Mol. Biol. 268, 170-184.
49. Gillespie, J. R. & Shortle, D. (1997) J. Mol. Biol. 268, 158-169.